Genome and transcriptome analyses in yeast

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6.1 years ago

JJ ▴ 710

Hi all,

I've been working with higher model organisms so far (mouse/human). Now I'd like to analyse non-model yeasts. I don't see an issue with using my standard analysis workflow for this organism as well:

Genome analysis: bwa-mem & GATK (although I need known SNPs for GATK - is there a better tool to call SNPs in yeast?)

Transcriptome analysis: STAR, featureCounts & voom/Limma

However, is there anything I should watch out for and how would you recommend performing pathway analyses? Maybe using KOBAS? Any advice is highly appreciated.

Thanks!

SNP rna-seq sequencing • 1.1k views

ADD COMMENT • link 6.1 years ago by JJ ▴ 710

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Hi JJ, not much help, but looks pretty good to me. My only remark is - I don't understand why you would need known SNPs? For example, the GATK germline pipeline (and as such any germline snp calling) recommends to use as many samples as you can, but doesn't require SNPs, afaik.

Cheers, C

ADD REPLY • link 6.1 years ago by Carambakaracho ★ 3.3k

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One needs known SNPs for the recalibration step. A workaround would be to take the output of the first SNP calling, recalibrate and the call SNPs again...

Have you used KOBAS before? Any tipps concerning the pathway analysis?

ADD REPLY • link 6.1 years ago by JJ ▴ 710

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